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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure and Function of the Zinc Binding Protein ZrgA from Vibrio cholerae

ATP binding cassette (ABC) transporters are the primary means by which bacteria acquire trace elements from the environment. They rely on solute binding proteins (SBPs) to bind the relevant substrate and deliver it to the integral membrane permease for ATP-powered import into the cytoplasm. SBPs of cluster A-I are known to facilitate the transport of essential metals zinc, manganese, and iron, and many have been characterized to date. A group of ABC transporter operons dubbed zinc-regulated genes (zrg) have recently been shown to transport zinc with putative SBPs (zrgA) bearing no homology to the classical cluster A-I family, and a recent crystal structure of a representative protein from Pseudomonas aeruginosa shows no structural similarity to classical SBPs. Thus, the ZrgA proteins appear to represent a newly discovered family of zinc SBPs widespread among Gram-negative bacteria, including human pathogens. Here, we have determined the crystal structure of ZrgA from Vibrio cholerae and characterized its zinc binding in vitro and function in vivo. We also assessed the role of a histidine-rich sequence that appears to be a hallmark of ZrgA proteins that is particularly long in V. cholerae ZrgA. The results show that the zrgA gene is critical to the function of the operon, consistent with a function as an SBP in this system. Further, the His-rich region is not essential to the function of ZrgA, but it does provide additional zinc binding sites in vitro. The structure and zinc binding data for ZrgA reveal interesting differences between it and its homologue from P. aeruginosa, illustrating diversity within this little-studied protein family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The photon content of the proton in the CT18 global analysis

Recently, two photon PDF sets based on implementations of the LUX ansatz into the CT18 global analysis were released. In CT18lux, the photon PDF is calculated directly using the LUX master formula for all scales, \mu μ . In an alternative realization, CT18qed, the photon PDF is initialized at the starting scale, \mu_0 μ 0 , using the LUX formulation and evolved to higher scales \mu(>\mu_0) μ ( > μ 0 ) with a combined QED+QCD kernel at \mathcal{O}(\alpha),~\mathcal{O}(\alpha\alpha_s) 𝒪 ( α ) , 𝒪 ( α α s ) and \mathcal{O}(\alpha^2) 𝒪 ( α 2 ) . In the small- x x region, the photon PDF uncertainty is mainly induced by the quark and gluon PDFs, through the perturbative DIS structure functions. In comparison, the large- x x photon uncertainty comes from various low-energy, nonperturbative contributions, including variations of the inelastic structure functions in the resonance and continuum regions, higher-twist and target-mass corrections, and elastic electromagnetic form factors of the proton. We take the production of doubly-charged Higgs pairs, (H^{++}H^{--}) ( H + + H − − ) , as an example of scenarios beyond the Standard Model to illustrate the phenomenological implications of these photon PDFs at the LHC.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2001

Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

Pohorille, Andrew↗
DOE OSTI2023

Structure and functional determinants of Rad6–Bre1 subunits in the histone H2B ubiquitin-conjugating complex

The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 ‘backside’. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6–Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6–Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6–Bre1 interaction through a novel interface that is important for their biochemical and biological responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural and functional analysis of the human cone‐rod homeobox transcription factor

Abstract The cone‐rod homeobox (CRX) protein is a critical K50 homeodomain transcription factor responsible for the differentiation and maintenance of photoreceptor neurons in the vertebrate retina. Mutant alleles in the human gene encoding CRX result in a variety of distinct blinding retinopathies, including retinitis pigmentosa, cone‐rod dystrophy, and Leber congenital amaurosis. Despite the success of using in vitro biochemistry, animal models, and genomics approaches to study this clinically relevant transcription factor over the past 25 years since its initial characterization, there are no high‐resolution structures in the published literature for the CRX protein. In this study, we use bioinformatic approaches and small‐angle X‐ray scattering (SAXS) structural analysis to further understand the biochemical complexity of the human CRX homeodomain (CRX‐HD). We find that the CRX‐HD is a compact, globular monomer in solution that can specifically bind functional cis‐regulatory elements encoded upstream of retina‐specific genes. This study presents the first structural analysis of CRX, paving the way for a new approach to studying the biochemistry of this protein and its disease‐causing mutant protein variants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2019

Structural and Functional Adaptation of the Vestibular Otolith to Altered Gravity from Microgravity to Hypergravity

Inertial acceleration and a change in head orientation with respect to gravity are sensed by mechanosensitive receptors in the inner ear otolith organs. These structures consist of calcium carbonate grains called otoconia that mechanically load the hair cell bundles and distribute the tangential shear force during movement, and changes in their density can alter hair cell sensitivity. A possible adaptive response to a chronic gravity change is a change in weight-lending otoconia. Another mechanism is a modification of the strength and number of synapses coupling the hair cells to nerve afferents that convey the signals into the brain. Here, we present the results obtained in 2 species exposed both to µG (microgravity) and hyper-gravity (HG). Adult toadfish, Opsanus tau, were exposed to µG (microgravity) in 2 shuttle missions and to 1.12-2.24G (force of gravity) [resultant] centrifugation for 1-32 days; readaptation was studied following 1-8 days after return to 1G. Results show a biphasic pattern in response to 2.24G: initial hypersensitivity, similar to that observed after µG (microgravity) exposure, followed by transition to a significant decrease at 16-32 days. Recovery from HG exposure is approximately 4-8 days. Two major pieces of information are still needed: vertebrate hair cell response to altered gravity and impact of longer duration exposures on sensory plasticity. To address the latter we applied electron microscopic techniques to image otoconia mass obtained from 1) mice subjected to 91-days of µG (microgravity) in the Mouse Drawer System (MDS) flown on International Space Station, 2) mice subjected to 91-days of 1.24G centrifugation on ground, and 3) mice flown on 2 shuttle missions. Images from MDS mice indicate a clear restructuring of individual otoconia, suggesting deposition to the outer shell. Images from their HG ground counterparts indicate the converse - an ablation of the otoconia mass. For 13-day exposures to µG (microgravity) mice otoconia appear normal. Despite the permanence of gravity in evolution the animal senses exposure to a novel, non-1G, environment and adaptive mechanisms are initiated - in the short term compensation is likely confined to the peripheral sensory receptors, the brain or both. For longer exposures structural modifications of the otolith mass may also result.

Otoconia↗
DOE OSTI2025

Functional and Structural Studies on the Esperamicin Thioesterase and Progress toward Understanding Enediyne Core Biosynthesis

Enediynes are among the most potent antitumor and antibacterial natural products. Studies on their biosynthetic pathways have identified a shared, linear polyene precursor generated from an iterative type I polyketide synthase (PKSE) as the source of the enediyne warhead. A key step is the release of this polyene from the PKSE by a discrete thioesterase (TE). Here, in this study, we used X-ray crystallography, site-directed mutagenesis, and heterologous coexpression of PKSEs and TEs to elucidate how enediyne TEs mediate the production of the polyene. We solved the structure of wild-type EspE7 from esperamicin producer Actinomodura verrucosospora. The substrate binding pocket was also defined upon serendipitous cocrystallization of an EspE7 mutant with a fatty acyl-CoA ligand. Structural data and in vitro activity assays with EspE7 mutants provide strong evidence that Glu68 in EspE7 and the analogous Glu residue in other enediyne TEs functions as a key catalytic residue, thus supporting a hydrolysis mechanism for enediyne TEs that aligns with that of Pseudomonas sp. 4-HB-CoA TE. Furthermore, combinations of 9- and 10-membered enediyne PKSEs and TEs produced 1,3,5,7,9,11,13-pentadecaheptaene (1) as the major product. Thus, the data further support previous conclusions that 1 serves as the sole precursor for the biosynthesis of all enediyne cores.

Enediynes↗
DOE OSTI2021

Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is a major maize pest in the United States causing significant economic loss. The emergence of field-evolved resistant WCR to Bacillus thuringiensis (Bt) traits has prompted the need to discover and deploy new insecticidal proteins in transgenic maize. In the current study we determined the crystal structure and mode of action (MOA) of the Vpb4Da2 protein (formerly known as Vip4Da2) from Bt, the first identified insecticidal Vpb4 protein with commercial level control against WCR. The Vpb4Da2 structure exhibits a six-domain architecture mainly comprised of antiparallel β-sheets organized into β-sandwich layers. The amino-terminal domains 1–3 of the protein share structural homology with the protective antigen (PA) PA14 domain and encompass a long β-pore forming loop as in the clostridial binary-toxB module. Domains 5 and 6 at the carboxyl-terminal half of Vpb4Da2 are unique as this extension is not observed in PA or any other structurally-related protein other than Vpb4 homologs. These unique Vpb4 domains adopt the topologies of carbohydrate-binding modules known to participate in receptor-recognition. Functional assessment of Vpb4Da2 suggests that domains 4–6 comprise the WCR receptor binding region and are key in conferring the observed insecticidal activity against WCR. The current structural analysis was complemented by in vitro and in vivo characterizations, including immuno-histochemistry, demonstrating that Vpb4Da2 follows a MOA that is consistent with well-characterized 3-domain Bt insecticidal proteins despite significant structural differences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

Here, we outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships - however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Systematic uncertainties from higher-twist corrections in DIS at large x

We investigate the systematic uncertainties and potential biases arising from the inclusion of large- x corrections to proton and deuteron deep inelastic scattering (DIS) data in global quantum chromodynamics (QCD) analyses. Using the CTEQ-JLab framework, we examine various approaches to implementing higher-twist corrections in nucleon structure functions and off-shell PDF modifications in deuteron targets. We analyze how these components interact and influence the determination of the d -quark PDF and the neutron structure function at large x . We find that it is very important to consider isospin-dependent higher-twist corrections in order to minimize implementation biases in the extracted quantities. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Systematic uncertainty of off-shell corrections and higher-twist contribution in DIS at large x

We study the systematic uncertainty and biases introduced by theoretical assumptions needed to include large-x DIS data in a global QCD analysis. Working in the CTEQ-JLab framework, we focus on different implementations of higher-twist corrections to the nucleon structure functions and of offshell PDF deformations in deuteron targets and discuss how their interplay impacts the extraction of the d -quark PDF and the calculation of the neutron structure function at large x.

Cerutti, Matteo↗
NASA NTRS1995

Electron density power spectrum in the local interstellar medium

Interstellar scintillation (ISS), fluctuations in the amplitude and phase of radio waves caused by scattering in the interstellar medium, is important as a diagnostic of interstellar plasma turbulence. ISS is also of interest because it is noise for other radio astronomical observations. The unifying concern is the power spectrum of the interstellar electron density. Here we use ISS observations through the nearby (less than or approximately =1 kpc) (ISM) to estimate the spectrum. From measurements of angular broadening of pulsars and extragalactic sources, decorrelation bandwidth of pulsars, refractive steering of features in pulsar dynamic spectra, dispersion measured fluctuations of pulsars, and refractive scintillation index measurements, we construct a composite structure function that is approximately power law over 2 x 10(exp 6) m less than scale less than 10(exp 13) m. The data are consistent with the structure function having a logarithmic slope versus baseline less than 2; thus there is a meaningful connection between scales in the radiowave fluctuation field and the scales in the electron density field causing the scattering. The data give an upper limit to the inner scale, l(sub o) less than or approximately 10(exp 8) m and are consistent with much smaller values. We construct a composite electron density spectrum that is approximately power law over at least the approximately = 5 decade wavenumber range 10(exp -13)/m less than wavenumber less than 10(exp -8)/m and that may extend to higher wavenumbers. The average spectral index of electron density over this wavenumber range is approximately = 3.7, very close to the value expected for a Kolmogorov process. The outer scale size, L(sub o), must be greater than or approximately = 10(exp 13) m (determined from dispersion measure fluctuations). When the ISS data are combined with measurements of differential Faraday rotation angle, and gradients in the average electron density, constraints can be put on the spectrum at much smaller wave numbers. The composite spectrum is consistent with a Kolmogorov-like power law over a huge range (10 or more decades) of spatial wavenumber with an infrared outer scale L(sub o) greater than or approximately 10(exp 18)m. This power-law subrange-expressed as ratio of outer to inner scales-is comparable to or larger than that of other naturally occurring turbulent fluids, such as the oceans or the solar wind. We outline some of the theories for generating and maintaining such a spectrum over this huge wavenumber range.

Armstrong, J. W.↗
NASA NTRS2013

The Galex Time Domain Survey. I. Selection And Classification of Over a Thousand Ultraviolet Variable Sources

We present the selection and classification of over a thousand ultraviolet (UV) variable sources discovered in approximately 40 deg(exp 2) of GALEX Time Domain Survey (TDS) NUV images observed with a cadence of 2 days and a baseline of observations of approximately 3 years. The GALEX TDS fields were designed to be in spatial and temporal coordination with the Pan-STARRS1 Medium Deep Survey, which provides deep optical imaging and simultaneous optical transient detections via image differencing. We characterize the GALEX photometric errors empirically as a function of mean magnitude, and select sources that vary at the 5 sigma level in at least one epoch. We measure the statistical properties of the UV variability, including the structure function on timescales of days and years. We report classifications for the GALEX TDS sample using a combination of optical host colors and morphology, UV light curve characteristics, and matches to archival X-ray, and spectroscopy catalogs. We classify 62% of the sources as active galaxies (358 quasars and 305 active galactic nuclei), and 10% as variable stars (including 37 RR Lyrae, 53 M dwarf flare stars, and 2 cataclysmic variables). We detect a large-amplitude tail in the UV variability distribution for M-dwarf flare stars and RR Lyrae, reaching up to absolute value(Δm) = 4.6 mag and 2.9 mag, respectively. The mean amplitude of the structure function for quasars on year timescales is five times larger than observed at optical wavelengths. The remaining unclassified sources include UV-bright extragalactic transients, two of which have been spectroscopically confirmed to be a young core-collapse supernova and a flare from the tidal disruption of a star by dormant supermassive black hole. We calculate a surface density for variable sources in the UV with NUV less than 23 mag and absolute value(Δm) greater than 0.2 mag of approximately 8.0, 7.7, and 1.8 deg(exp −2) for quasars, active galactic nuclei, and RR Lyrae stars, respectively. We also calculate a surface density rate in the UV for transient sources, using the effective survey time at the cadence appropriate to each class, of approximately 15 and 52 deg(exp −2 yr−1 for M dwarfs and extragalactic transients, respectively.

Gezari, S.↗
NASA NTRS2001

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Non-NASA Center↗
NASA NTRS1976

Thermodynamics of two-dimensional plasmas or discrete line vortex fluids

The equilibrium properties of a two-dimensional plasma are examined theoretically within the framework of the random-phase approximation. The guiding-center case is of most interest because of the formal equivalence to two-dimensional discrete-line vortex fluids and because of the formal admissibility of negative temperatures. Using a judicious treatment of the periodic boundary conditions, extensive thermodynamics for nonnegative temperatures and a new value for the energy at which the temperature becomes negative are found. An explicit form for the structure function is derived and compared with the result of a Monte Carlo calculation. Good agreement is found for the negative-temperature-threshold prediction and for the general shape of the structure function. An equilibrium energy spectrum is calculated, which for positive temperatures, is the Debye-Hueckel result; for negative temperatures, it predicts an enhanced excitation of the lowest mode, corresponding to macroscopic charge separation.

Seyler, C. E., Jr.↗
DOE OSTI2022

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure and function of bacteriophage CBA120 ORF211 (TSP2), the determinant of phage specificity towards E. coli O157:H7

The genome of Escherichia coli O157:H7 bacteriophage vB_EcoM_CBA120 encodes four distinct tailspike proteins (TSPs). The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure. We report the 1.9 Å resolution crystal structure of TSP2 (ORF211), the TSP that confers phage specificity towards E. coli O157:H7. The structure shows that the N-terminal 168 residues involved in TSPs complex assembly are disordered in the absence of partner proteins. The ensuing head domain contains only the first of two fold modules seen in other phage vB_EcoM_CBA120 TSPs. The catalytic site resides in a cleft at the interface between adjacent trimer subunits, where Asp506, Glu568, and Asp571 are located in close proximity. Replacement of Asp506 and Asp571 for alanine residues abolishes enzyme activity, thus identifying the acid/base catalytic machinery. However, activity remains intact when Asp506 and Asp571 are mutated into asparagine residues. Analysis of additional site-directed mutants in the background of the D506N:D571N mutant suggests engagement of an alternative catalytic apparatus comprising Glu568 and Tyr623. Finally, we demonstrate the catalytic role of two interacting glutamate residues of TSP1, located in a cleft between two trimer subunits, Glu456 and Glu483, underscoring the diversity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.

59 BASIC BIOLOGICAL SCIENCES↗